A fresh High Court challenge could be launched after the Immigration Minister indicated he would personally apply a "national interest" test for permanent protection applications from people who arrive without a visa.

"[It will] essentially defy the clear will of Parliament and the rule of law in this country," he said.

Last month's High Court decision was sparked by Mr Manne's client, a 16-year-old unaccompanied boy whose case is still before the court.

He said while the national interest test exists in regulations, it has not been raised in the case before.

However, Mr Manne said he has been given examples of why granting a visa may not be in the national interest.

"For reasons which include that this could erode the community's confidence in the effective and orderly management of Australia's migration program, that it could undermine the integrity of Australia's visa systems and also Australia's sovereign right to protect its borders," he said.

"It also outlines another reason and that is that people, like our client, should not be rewarded with the same permanent visa outcomes that people who, it said, abide by Australia's visa requirements may be entitled to."

He said if there are attempts to deny his client a visa on national interest grounds, a challenge would be launched.

"It also stands to reason that over the years tens of thousands of people have been granted protection visas in this country without the national interest regulation being invoked to refuse their applications for visas and certainly if any steps are taken to refuse our client's application, we certainly intend to launch a further challenge to that in the High Court," he said.

"It is clearly in the national interest for the Government to grant a protection visa to a person who's been found to be a refugee and has met all of the other relevant criteria and that has been the longstanding practice under successive Australian governments.

"This is not a question about a person not being granted a temporary protection visa. This is about refusing a protection visa altogether and leaving our client, a 16-year-old boy who's been found to be a refugee and potentially thousands of other people found to be refugees, in limbo in the community or in indefinite detention."

In a statement, Mr Morrison said: "The policy of the Australian Government is that those who arrived illegally by boat or plane... should only be granted a temporary visa."

"This policy forms part of a suite of measures that have been critical to the Government's success to date in preventing maritime people smuggling ventures as part of Operation Sovereign Borders.

"The Government will continue to implement this policy consistent with the powers established under the Migration Act and national interest."

An act of desperation: Hanson-Young

Greens Senator Sarah Hanson-Young said the Minister was thumbing his nose at the will of the Parliament and the ruling of the High Court.

"This is clearly an act of desperation by Mr Morrison," she said.

"It is him [and] his department acting in a way that seems to be, not just above the law, but above the Parliament."

There have been reports in recent days that two asylum seeker boats have been intercepted by Australian authorities in the Indian Ocean and that the passengers of one of the boats are set to be transferred to the Sri Lankan navy at sea.

Mr Morrison refused to confirm the existence of the boat and would not address questions about whether the asylum seekers would be handed over to Sri Lankan authorities.